There are a few oddities that haven't made it to Amazon yet. All older books, and I'm not actually sure why. But you can spot them on the Baen site because they're still priced at the old price of $4.00. I suspect there's some sort of permissions issue that doesn't let them sell them except on the Baen site. But there really are only a few.

Baen isn't the publisher for all the ebooks on their website.
Their ebookstore carries titles from other publishers; some it's because the author retains ebook rights and the other publisher holds print rights.
In at least one occasion, the monthly bundle was used to distribute an optional book, effectively a free promo.
They're open-minded and flexible.